Characterisation and validation of novel biomarkers and therapeutic candidates in paediatric inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic and currently incurable condition. Abnormal immune responses to the resident gut microbiome can drive or exacerbate IBD, however, these relationships are yet to be fully elucidated. Until recently, microbiome-based studies in IBD have predominantly been restricted to culture-independent sequencing-based analyses, typically of faecal samples. This reliance on both faecal samples and sequencing alone has limited understanding of host-microbiome interactions at the intestinal site of disease. This thesis defines key IBD-associated functional bacterial clades from within the patient microbiome, by combining shotgun metagenomic sequencing, bacterial culturing and host transcriptomic analysis with detailed experimental validation.